Re: [ccp4bb] Rfactor and Rfree not coming below 0.4

2017-01-21 Thread Eleanor Dodson
When you have some reasonable map features but such a high R factor my first guess is you have the spce group wrong - P21212 instead of P212121 or something. It can mean you have half the reflections corret and half not. Go back and check the data processing carefully (CCP4 GUI2 gives an excellent

Re: [ccp4bb] POINTLESS error: "NormaliseInRuns::apply Unused run 0"

2017-01-21 Thread Eleanor Dodson
can you send the whole log file? Somehow the XDS input isnt agreeing with pointless expectations, so I suspect no reflections have been read Eleanor On 20 January 2017 at 23:41, Joseph Brock wrote: > Dear ccp4 experts, > > I am trying to use the ccp4i Pointless, Aimless, Ctruncate application to

Re: [ccp4bb] Rfactor and Rfree not coming below 0.4

2017-01-21 Thread Bernhard Rupp
If you solved by MR, this sounds like the description of a model biased map. Be aware that the density graph in coot needs to be properly scaled (cf. Dale’s response on absolute density scale). Extensions->Refine->Set density graph weight. If you see no parts that are discernably different fro

Re: [ccp4bb] How to align maps in CCP4

2017-01-21 Thread Denis Rousseau
I want to align maps from two different proteins and then use COOT to calculate a difference map. With the superpose function in Phenix the alignment of the pdb files only uses one chain (I have 13). I would like to do the same type of SSM superposition that is available in COOT but to drag the

Re: [ccp4bb] How to align maps in CCP4

2017-01-21 Thread Eleanor Dodson
This is quite possible but I am at home and have forgotten the menu item.. is it under the Draw widget? Can check on Monday! Eleanor On 21 January 2017 at 18:58, Denis Rousseau wrote: > I want to align maps from two different proteins and then use COOT to > calculate a difference map. With the s

Re: [ccp4bb] How to align maps in CCP4

2017-01-21 Thread Christian Roth
In Coot it is under Extensions--> Maps --> Transform map by lsq model fit Please correct me if it is not what you mean Eleanor Cheers Christian On Sat, Jan 21, 2017 at 8:22 PM, Eleanor Dodson wrote: > This is quite possible but I am at home and have forgotten the menu item.. > is it under th

Re: [ccp4bb] How to align maps in CCP4

2017-01-21 Thread Eleanor Dodson
Thank you Christian - thats what I meant.. E On 21 January 2017 at 20:09, Christian Roth wrote: > In Coot it is under Extensions--> Maps --> Transform map by lsq model fit > Please correct me if it is not what you mean Eleanor > > Cheers > > Christian > > > On Sat, Jan 21, 2017 at 8:22 PM, Elea